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This file describes the compressed dataset and code files contained in this repository.

Three files include dataset files (Datasets 1-3) and two include codes for replicating the analysis: Dataset 1 (Mr. Bayes and BEAST2 codes within folders for each analysis conducted) and Dataset 4 (containing R scripts for all the other analyses).

Dataset 1:  Original and updated morphological character lists and the updated morphological dataset in Nexus format.

Dataset 2: Includes input Nexus files containing the morphological dataset with all Mr. Bayes commands with comments for each analysis within the respective analysis folders, or the XML file to replicate BEAST2 analyses. Output files include log files, tree files, and all other outputs from Mr. Bayes and BEAST2.

Dataset 3: Input files and tables for running all R scripts (available as Dataset 4), and outputs from statistical analysis in R (e.g., summary statistics, Gower distance matrix, among others).

Dataset 4: Includes 6 R scripts to replicate all analyses prior to and subsequent to evolutionary tree inference. Each R script includes detailed comments to guide any reader interested on replicating the analysis herein, or utilizing our protocols for their own datasets (e.g., guides on performing character partitioning and assessing the strength of selection):

CharPartitioning_Tetrapods.R: Customized script for the new protocol presented in this study to automatically detect character partitions based on the Gower distance metric and graphic cluster visualization using t-SNEs. The phylogenetic data matrix can be imported by saving a copy of the dataset as a .csv file (as in the example provided), or using functions available in the package Claddis to import the phylogenetic data matrix into R and subsequently converting it into matrix file.

NewFUNCTIONS.R: New functions developed by Jo�lle Barido-Sottani (see references therein) or by us to import tree files from BEAST2 and Mr. Bayes with metadata embedded (e.g., evolutionary rates), and to remove "dummy taxa" introduced by the "treeWoffset" operator from BEAST2.

RWTY_Tetrapods.R: Script for the RWTY back to extract diagnostic parameters from all analyses.

StatTestsy&Plots_Rates_Tetrapods.R: Script to perform statistical tests, output summary statistic values, and plot graphs related to morphological evolutionary rates obtained from the final analyses.

StatTests&Plots_FBD_Tetrapods.R: Script to perform statistical tests, output summary statistic values, and plot graphs related to FBD parameters outputs (net diversification, relative extinction, and relative fossilization) obtained from the final analyses.

StatsTests&Plots_SelectionStrength_Tetrapods.R: Customized script for the new protocol presented in this study to assess the strength of natural selection inferred from clock-based evolutionary rates using morphological data (applicable to living and/or extinct species).

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